Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Evol Bioinform Online. 2013;9:127-36. doi: 10.4137/EBO.S11250. Epub 2013 Mar 10.
The expression levels of bacterial genes can be measured directly using next-generation sequencing (NGS) methods, offering much greater sensitivity and accuracy than earlier, microarray-based methods. Most bioinformatics software for estimating levels of gene expression from NGS data has been designed for eukaryotic genomes, with algorithms focusing particularly on detection of splicing patterns. These methods do not perform well on bacterial genomes.
Here we describe the first software system designed explicitly for quantifying the degree of gene expression in bacteria and other prokaryotes. EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) processes the raw data from an RNA-seq experiment on a bacterial or archaeal species and produces estimates of the expression levels for each gene in these gene-dense genomes.
The EDGE-pro tool is implemented as a pipeline of C++ and Perl programs and is freely available as open-source code at http://www.genomics.jhu.edu/software/EDGE/index.shtml.
使用下一代测序 (NGS) 方法可以直接测量细菌基因的表达水平，其灵敏度和准确性比早期基于微阵列的方法高得多。用于从 NGS 数据估计基因表达水平的大多数生物信息学软件都是为真核基因组设计的，其算法特别侧重于检测剪接模式。这些方法在细菌基因组上的表现不佳。
在这里，我们描述了第一个专门用于量化细菌和其他原核生物基因表达程度的软件系统。EDGE-pro（用于原核生物的基因表达估计）处理来自细菌或古细菌物种的 RNA-seq 实验的原始数据，并为这些基因密集型基因组中的每个基因生成表达水平的估计值。
EDGE-pro 工具实现为 C++和 Perl 程序的流水线，并且作为开源代码免费提供，网址为 http://www.genomics.jhu.edu/software/EDGE/index.shtml。
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